Good (and Bad) Bacteria in Flour: Before and After Fermentation

…”the raw materials we use in fermentation can introduce different microbes depending on how those materials were produced. A recent study in Italy of sourdough fermentation demonstrated that organic vs. conventional farming can affect the quality of sourdough bread.”

Studies are finding that the various farming techniques influence the nutritional content of the end result food.  The study in Italy processed (durum) wheat four ways and used the flour in a sourdough recipe, …”look[ing] at how the farming practices impacted not only the quality of the flour that was milled from the wheat, but also the composition of the microbes in the flour before and after being used for sourdough fermentation.”

  • Conventional (fertilizers and pesticides applied)
  • Organic with cow manure
  • Organic with green manure (ground plants tilled in to soil)
  • No inputs (no fertilizer or pesticides)

When all was said and done, they tested everything, paying particular attention to the final product: bread.  Since they wanted to find out which flour production was the best for sourdough bread, the study said “They were particularly interested in the identities of lactic acid bacteria since they play a significant role in sourdough fermentation, and therefore plated out samples of dough before and after fermentation on a special medium to identify specific strains of lactic acid bacteria.” Lactic acid is what gives sourdough bread the sour taste.  Typically, the healthier the sourdough starter, the more the flour ferments.


  • Organic farming practices made the best bread
  • No Input also made good bread (firm structure) BUT the crop didn’t produce enough wheat!

The commentator on the study, Benjamin Wolfe, highlighted one significant flaw of this Italian study: no one did a sensory analysis of the bread’s taste, which is a HUGE component in sourdough bread making!

I’ve made plenty of sourdough breads and, aside from just looking at it, the first bite tells all.  When your face puckers, it could be from a great fermented starter or an imbalanced rise time due to the specific flour used.

The results that I think are neat is the list of the seven most abundant bacteria groups in each flour, both before and after fermentation.  I find this interesting because certain good gut bacteria can aid in weight loss more than others; it has been hard to identify and track down the specific “jobs” of bacteria.

Out of curiosity, I Googled the bacteria Pantoea since it is in high amounts in the flour but is significantly removed after the process of fermentation.  Wow.

The National Center for Biotechnology Information (NCBI) published one study that isolated pantoea found in infant formula and its effects on infants specifically in the NICU.  According to the source, pantoea “is commonly found in the ecological niches such as water, soil, sewage, seeds, vegetables, feculent material and foodstuffs, as well as reported as both commercial and opportunistic pathogens of animals and humans. This opportunistic pathogen isolated from clinical specimens including blood, wounds, urine, throat, and internal organs.”

It is an “opportunistic pathogen.” Another NCBI study describes these “as organisms that can become pathogenic following a perturbation to their host (e.g., disease, wound, medication, prior infection, immunodeficiency, and ageing). These opportunists can emerge from among the ranks of normally commensal symbionts (e.g., Streptococcus pneumoniae and Staphylococcus aureus) or from environmentally acquired microbes (e.g., Pseudomonas aeruginosa and Burkholderia cepacia). Many more pathogens are recognized as opportunists in the sense that although they regularly cause disease in healthy humans, they are also zoonotic and exploit numerous other hosts (e.g., Bacillus anthracis and rabies virus).”

Going back to the original study on pantoea bacteria present in infant formula done on NICU infants—those who are susceptible to infections, the findings were disturbing.  The study noted a high amount of infections: “In recent years a remarkable increase in nosocomial infections has been reported especially in neonatal intensive care unit (NICU), intensive care units (ICU) and oncology departments. Underlying diseases, low-birth-weight, immunocompromised immune system, cancer chemotherapy, and intravenous catheterization can be predisposing factors in cases of infections due to unusual microorganisms, including P. agglomerans.”  

So, studies are confirming that this opportunistic pathogen is causing harm to preemie babies exposed to the pathogen through powdered infant formula, which is made with (any type) of wheat (farming systems chart from sourdough study). Gulp.  But, it is completely eliminated from the source wheat after fermentation….sigh.

Intrigued, I looked into the other 2 bacteria present in medium abundance in the wheat only prior to fermentation.  Pseudomonas bacteria is another pathogen, with “more severe infections occur[ing] in people who are already hospitalized with another illness or condition” AKA preemies in a NICU being fed infant formula made with a wheat with the bacteria present?!  “Infections can be severe in patients whose immune systems are already compromised,” such as a preemie or older person with a catheter or ventilator.

One strain of the Leuconostoc bacteria is classified as another “unusual opportunistic, vancomycin-resistant pathogen” linked to infections “especially in debilitated” patients with “prolonged hospital stays.”

In contrast, fermenting flour actually strengthens the leuconostoc bacteria and it is present in significant amounts in the soil that was left untreated or tilled. Usually, however, individuals who have access to fermented sourdough bread are not hospitalized, but it brings in to question the potential implications for someone who is starting to eat healthy but still has an unhealthy gut.  Food for thought.

“The genus Leuconostoc belongs to the group of lactic acid bacteria. They are a group of related Gram-positive, non-sporulating bacteria that produce lactic acid as a result of carbohydrate fermentation….Like the lactic acid bacteria, leuconostocs need complex media due to their multiple demands for amino acids, peptides, carbohydrates, vitamins and metallic ions. They represent about 12% of lactic acid bacteria isolated from various ecosystems, mostly from plant materials.”

Another NCBI study that was identifying “the capacity of potentially probiotic strains from six bacterial genera (Streptococcus, Lactobacillus, Bifidobacterium, Lactococcus,Leuconostoc and Propionibacterium)” confirmed that these bacteria promoted “the activation of antimicrobial immune responses.” The bacteria I put in bold are the only three high to very high in abundance in fermented flour noted in the Italian study and are not found in the flour prior to fermentation in significant amounts.

The study came across a new, “novel” finding: Leuconostoc strains working together with (another) probiotic “were extremely good inducers of these Th1 type cytokines” in the gut for treating allergies and respiratory infections.   This bacteria is present in fermented flour, which is sourdough, and very minimally before fermentation.

My research take-away? Any type of farming practice introduces one strong pathogen, pantoea, into the body, which be especially dangerous to preemies and the elderly.  This pathogen is completely eliminated when the flour is fermented.   One strain of leuconostoc is another pathogen for the same population, but is beneficial when combined with other probiotic bacteria.   After fermentation, the flours have an abundance of bacteria that are beneficial in the gut.  It seems that fermentation has all positive effects, regardless even of farming systems.


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